[gmx-users] Conversion of charmm36 parameters from namd to gromacs

Daniel Bauer bauer at cbs.tu-darmstadt.de
Mon Dec 4 20:35:24 CET 2017

Unfortunatly It seems like my university has no contract to access this
paper so I cant check the SI.

The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted
to better match the free energy of solvation in NMA).

On  12/04/2017 07:53 PM, Justin Lemkul wrote:
> On 12/4/17 12:21 PM, Daniel Bauer wrote:
>> Hello,
>> I finally found my error in the conversion. As always, the devil is in
>> the detail. I was under the assumption that parameters listed in the
>> original forcefield files (toppar) are also sigma and epsilon values.
>> However, as you know, the original files list Rmin values (and not
>> sigma).
>> With the correct conversion term:
>> eps = Rmin/(10*2^(1/6))
>> I can now reproduce the conversion of the numbers from the charmm
>> implementation to gromacs (and thus know how to apply my NBFIX for this
>> value).
> I don't know what NBFIX you might have, but FYI there is a value that
> will become official in the next release of the force field. We've
> validated it against proteins and nucleic acids. See the SI of
> http://dx.doi.org/10.1128/AAC.01572-17
> -Justin


Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
bauer at cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.

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